Table 1. Metagenomic methods: community profiling vs functional metagenomics
Common Features
Unique to community profiling
Unique to functional metagenomics
DNA obtained directly from a
wound sample; culture
independent
Marker genes such as 16S rRNA gene
from a community of bacteria, or 18S
rRNA and internal transcribed spacer
(ITS) genes for fungi
Can provide genomic DNA from a
community of microorganisms. Applicable
to all microorganisms including bacteria,
fungi, viruses and archaea
Need to remove human host DNA
contamination
PCR primers amplify only marker gene
fragments from targeted microbes,
excluding DNA from the human host
To avoid biases human DNA must be
removed after sequencing through
computational methods
Sequenced using high-throughput
sequencing technologies
Sequencing errors in highly conserved
marker genes can lead to incorrect species
assignment
Taxonomic assignment based on multiple
genes from genomic DNA can lead to more
accurate taxonomic community profiles
Reduction in the overall cost of
sequencing
Sequencing is directed at only microbial
marker genes, making sequencing more
cost effective
Sequencing can be more cost-prohibitive due
to human host contamination (~90% of DNA
in wound samples)
Data represent a community of
microorganisms and reflect
organismal diversity and
abundance
Community profile is based only on
taxonomy
Community profile is based on taxonomy
and function, indicating the metabolic
potential of a microbial community
Less than 1% of organisms are
known, leading to incomplete
annotation
Closely-related organisms are
indistinguishable based on marker gene
sequences alone. Not all bacteria are
represented in databases of known 16S
rRNA genes or 18S and internal
transcribed spacer (ITS) for fungi
Not all microbial genomes exist in databases
of known species leading to difficulty in
assigning sequences to discrete organisms
Has potential for serendipitous
discovery of clinically relevant
organisms or function
Novel variations in the hypervariable
regions of marker genes can indicate new
species
Genomes of unknown organisms can be
reconstructed from genomic fragments in
metagenomes, providing insights into new
species and function
Has potential to find humanmicrobe interactions
Can find links between microbial
community composition and clinical
factors or patient outcomes
Can find links between microbial community
composition & function and clinical factors
or patient outcomes